Porous membrane waveguide sensors and sensing systems therefrom for detecting biological or chemical targets

ABSTRACT

A sensor for sensing at least one biological target or chemical target is provided. The sensor includes a membrane includes a membrane material that supports generation and propagation of at least one waveguide mode, where the membrane material includes a plurality of voids having an average size&lt;2 microns. The sensor also includes at least one receptor having structure for binding to the target within the plurality of voids, and an optical coupler for coupling light to the membrane sufficient to generate the waveguide mode in the membrane from photons incident on the optical coupler.

CROSS REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of Provisional Application Ser. No.61/196,502 entitled “POROUS MEMBRANE WAVEGUIDE SENSORS AND SENSINGSYSTEMS THEREFROM FOR DETECTING BIOLOGICAL OR CHEMICAL TARGETS”, filedOct. 17, 2008, which is herein incorporated by reference in itsentirety.

FEDERAL RIGHTS

The U.S. Government has certain rights to embodiments of the presentinvention based on National Science Foundation Grant ECCS-0746296 andArmy Research Office Grant W911NF-08-1-0200.

FIELD OF THE INVENTION

The invention pertains to membrane-based sensors for detecting chemicalor biological targets.

BACKGROUND

The detection of biomolecules and certain chemicals is important for awide variety of applications. Applications for biomolecule sensinginclude medical diagnostics, food safety, and anti-bioterrorism.Conventional biosensors often include fluorescent reporter labels togenerate a detection signal.

Label-free biosensors and chemical sensors can directly measureunmodified samples without the need for reporter molecules. Suchlabel-free sensors generally operate based on a change in refractiveindex due to affinity binding events of biomolecules or chemicals. Forexample, biomolecules immobilized on the surface of surface plasmonresonance (SPR), fiber optic, and planar waveguide sensors interact withthe evanescent field of either the surface plasmon or waveguide mode andcause a refractive index change near the surface of these sensors.However, these evanescent wave sensors are limited in sensitivity,especially for small molecule (e.g. 200-1,000 Daltons) detection, sincethe surface area is small and the interaction between biomolecules orchemicals and the electromagnetic field is generally fairly weak.

SUMMARY

This Summary is provided to comply with 37 C.F.R. §1.73, presenting asummary of the invention to briefly indicate the nature and substance ofthe invention. It is submitted with the understanding that it will notbe used to interpret or limit the scope or meaning of the claims.Embodiments of the present invention describe porous membrane waveguidesensors and sensing systems for detecting biological or chemicaltargets.

In a first embodiment of the invention, a sensor for sensing at leastone biological target or chemical target is provided. The sensorincludes a membrane comprising a membrane material that supportsgeneration and propagation of at least one waveguide mode, the membranematerial comprising a plurality of voids having an average size<2microns. The sensor also includes at least one receptor having structurefor binding to the target immobilized within the plurality of voids, andan optical coupler for coupling light to the membrane sufficient togenerate the waveguide mode in the membrane from photons incident on theoptical coupler.

In a second embodiment of the invention, a sensor chip is provided. Thesensor chip includes an optically transparent support material and amembrane comprising a membrane material on the support that supportsgeneration and propagation of at least waveguide mode. The membranematerial includes a plurality of voids having an average size<2 microns.The sensor chip also includes at least one receptor having structure forbinding to the target immobilized within the plurality of voids, and acladding layer interposed between the optically transparent supportmaterial and the membrane.

In a third embodiment of the invention, a sensing system is provided.The system includes a sensor for sensing at least one biological targetor chemical target. The sensor includes a substrate support layer and amembrane comprising a membrane material that supports generation andpropagation of at least one waveguide mode on the support layer. Themembrane material includes a plurality of voids having an average size<2microns. The sensor also includes at least one receptor having structurefor binding to the target immobilized within the plurality of voids. Thesystem also includes an optical block operable for coupling light to themembrane sufficiently to generate the waveguide mode in the membranefrom photons propagating in the optical block. The system also includesa light source for providing the photons, and a light detector fordetecting the photons that are reflected by the optical block.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a depiction of a first exemplary sensor system including aporous membrane waveguide sensor according to an embodiment of theinvention for sensing at least one biological target or chemical target.

FIG. 2 is a depiction of a second exemplary sensor system including aporous membrane waveguide sensor according to an embodiment of theinvention for sensing at least one biological target or chemical target.

FIG. 3 is a depiction of a third exemplary sensor system including aporous membrane waveguide sensor according to an embodiment of theinvention for sensing at least one biological target or chemical target.

FIG. 4 is a depiction of a fourth exemplary sensor system including aporous membrane waveguide sensor according to an embodiment of theinvention for sensing at least one biological target or chemical target.

FIG. 5 shows a scanning electron microscopy (SEM) image of a fabricatedporous silicon membrane for a sensor in accordance with an embodiment ofthe invention, evidencing voids.

FIG. 6 shows the measurement of the waveguide mode of a fabricatedporous silicon membrane for a sensor in accordance with an embodiment ofthe invention, for simulated and experimental values.

FIG. 7 shows the experimental resonance shifts after the fabricatedsensor in accordance with an embodiment of the invention was exposed todifferent concentrations of complementary DNA.

FIG. 8 shows an x-y plot 800 of reflectance as a function of resonanceangle for a sensor in accordance with an embodiment of the invention.

FIGS. 9A and 9B show the theoretically calculated sensitivity andcorresponding resonance angles, as a function of the porosity, for a1.55 m thick polymer-cladded porous silicon membrane waveguide layer inaccordance with an embodiment of the invention.

FIG. 10 is a depiction of an alternate exemplary sensor system includinga porous membrane waveguide sensor according to an embodiment of theinvention for sensing at least one biological target or chemical target.

DETAILED DESCRIPTION

The present invention is described with reference to the attachedfigures, wherein like reference numerals are used throughout the figuresto designate similar or equivalent elements. The figures are not drawnto scale and they are provided merely to illustrate the instantinvention. Several aspects of the invention are described below withreference to example applications for illustration. It should beunderstood that numerous specific details, relationships, and methodsare set forth to provide a full understanding of the invention. Onehaving ordinary skill in the relevant art, however, will readilyrecognize that the invention can be practiced without one or more of thespecific details or with other methods. In other instances, well-knownstructures or operations are not shown in detail to avoid obscuring theinvention. The present invention is not limited by the illustratedordering of acts or events, as some acts may occur in different ordersand/or concurrently with other acts or events. Furthermore, not allillustrated acts or events are required to implement a methodology inaccordance with the present invention.

Embodiments of the invention describe porous membrane waveguide sensorsfor sensing at least one biological target or chemical target. Theporous membrane waveguide sensors comprise a membrane material thatsupports generation and propagation of at least one waveguide mode,wherein the membrane includes a plurality of voids having receptormolecules therein. As known in the art, support of waveguide modes is acharacteristic of an optical waveguide that can comprise a dielectric ora semiconductor material. As defined herein, the term “membrane” as usedin “porous membrane” refers to a layer having a thickness≦10 microns.Moreover, the term “porous” as used herein in “porous membrane” refersto layer having a plurality of voids over at least a portion of the areaand the thickness of the layer, wherein the effective refractive indexof portion including the voids is≦90% of the refractive index of thebulk (non-void comprising) membrane material.

As defined herein, the term “waveguide mode”, refers to both guided andleaky modes in an optical waveguide. A guided, bound, or trapped mode inan optical waveguide is a mode that (a) has an electric field thatdecays monotonically in the transverse direction everywhere external tothe core and (b) does not lose power to radiation. A leaky mode ortunneling mode in an optical waveguide is a mode having an electricfield that decays monotonically for a finite distance in the transversedirection but becomes oscillatory everywhere beyond that finitedistance. Such a mode gradually “leaks” out of the waveguide as ittravels down it, producing attenuation.

There is a wide variety of different optical waveguiding materials thatsupport at least one waveguide mode, with the only requirements beingthat the material is surrounded by one or more lower refractive index“cladding” materials and that the waveguide material does not completelyabsorb or absorb too much light at the wavelength to be excited. As usedherein, the term “light”, is not limited to visible light, and generallyalso includes the ultraviolet, infrared and a portion of the microwaverange. A few non-limiting examples of waveguide materials that can beused with embodiments of the invention as the membrane material includecertain polymers, glass, certain nonlinear materials such as lithiumniobate, and semiconductor materials. Semiconductor materials caninclude as column IV semiconductors, III-V semiconductors, IV-VIsemiconductor materials, or any variants or mixtures thereof. In someembodiments, metal comprising materials can also be used, such asoptical metal oxide materials.

In the various embodiments of the invention, the porous membranematerial can be formed in a variety of ways. For example, in someembodiments of the invention, the porous membrane material can be formedby applying an etching agent to a non-porous material in order to formvoids in the non-porous material. In some embodiments of the invention,the voids in porous membrane material can be formed during formation ofthe porous membrane material. For example, a material or a process forforming a material can be utilized that is susceptible to the formationof voids. Alternatively materials or processes that result in structureshaving voids can also be used, such as carbon nanotubes.

In order to support guided and leaky mode propagation, the voids in themembrane material should generally have an average size that issignificantly less than the wavelength of light propagating therein. Inthe exemplary case of 1550 nm (1.55 micron) light, the void size shouldgenerally be<1 micron, such as<0.5 micron. However, for most waveguidematerials the membrane material can generally support light propagationat much longer wavelengths, which allows for larger void sizes. However,obtaining compact, cost-effective light sources for longer wavelengths(e.g. 10 microns) may pose a challenge.

The thickness of the porous membrane generally determines the number ofguided modes supported, with more modes being supported for higherthicknesses. In most embodiments of the invention, the membranethickness is between 100 nm and several microns thick, such as 5microns, for guided modes. For leaky modes, the membrane thickness canbe thinner. The minimum membrane thickness generally depends on therefractive index of the cladding and the membrane material and thewavelength of light used, with the minimum thickness for an exemplaryporous silicon waveguide and polymer cladding being on the order of afew hundred nanometers. There are characteristic equations that can besolved to determine the minimum membrane thickness based on theseparameters. Generally, as the refractive index contrast between theporous membrane waveguiding layer and cladding layer decreases, theminimum membrane thickness increases. For example, in traditional fibertechnology where the refractive index contrast can be on the order onepercent, the minimum membrane thickness generally being on the order ofa few to several microns.

An increase in the number of waveguide modes contributes to modaldispersion losses and the various higher order waveguide modes are notquite as well confined as the zero-order mode. Another significantdrawback of a very thick porous membrane is generally the diffusion timerequired for receptor molecules to diffuse into the depth of the porousmembrane.

At least one receptor having structure for binding to the target isimmobilized within the plurality of voids. The receptors can comprisereceptors such as a chemical receptor, a bioreceptor, a polymer, abiopolymer, a molecular imprint polymer, a biomimetic, an antibody, anenzyme, a cell receptor, a molecular print assay, or a nucleic acid. Thesensor also includes one or more optical blocks operable for couplinglight to the porous membrane sufficient to generate at least onewaveguide mode in the membrane material from photons incident on theoptical block. The optical coupler can comprise a prism or a gratingcoupler, as illustrated below in FIGS. 1-4.

In typical operation, when the target is present and exposed to thereceptors that are in the voids, the target becomes bound to thereceptors, thus increasing the refractive index of the porous membrane.The change in the refractive index of the porous membrane changes thewaveguide mode dispersion characteristics including a change in thewaveguide resonance angle which corresponds to the angle at which thelight in the optical coupler couples into the porous membrane, and achange in the intensity of light propagating in the porous membranewaveguide. Thus, if the target molecules bind to the receptors, thentheir presence can be detected by a change in resonance angle or achange in intensity of light exiting the porous membrane waveguide.Moreover, the change in waveguide resonance angle and change inintensity has been found to be related to the concentration of thetarget, such as being nearly linear with the target concentration. If abroadband source or tunable light source is used, a change in resonancewavelength could also be monitored to determine when targets are boundto receptors.

FIG. 1 is a depiction of an exemplary sensor system 100 including aporous membrane waveguide sensor 110 according to am embodiment of theinvention for sensing at least one biological target or chemical target.Sensor 110 includes a porous membrane 105 comprising a membrane materialthat supports generation and propagation of at least one waveguide mode.The porous membrane 105 includes a plurality of voids 107 having anaverage size<5 microns, wherein at least one receptor 108 which has astructure for binding to the target is immobilized within the voids 107.In some embodiments of the invention, the voids can comprise cylindricalvoids. In such embodiments, the voids can have a diameter that is from 5to 100 nm and the receptors line the void surface. The receptors willgenerally be immobilized onto the surfaces of the voids.

Sensor 110 includes an optical coupler shown as a prism 115 for couplinglight (shown as light in) to the porous membrane 105 from a light source125 (e.g. laser) sufficient to generate at least one waveguide mode forlight propagating through membrane 105 (shown as light path) from thelight transmitted by the prism 115. Absorption losses are minimized bysensor 110 because light is coupled to the porous membrane waveguide 105through a low loss path comprising prism 115 and cladding 120, incontrast to arrangements that require coupling of light through highloss paths such as through thick support layers such as 500 micron thicksilicon substrates. In arrangements using silicon substrates, lowerdoped silicon substrates can be used to reduce losses in the visiblespectrum. Moreover, porous membrane 105 is the only porous layer insensor 110. Sensor 110 (and sensor 210 described below relative to FIG.2) have the advantage over sensors that have two (or more) porous layerssince all target molecules exposed to the sensor 110 remain in theporous membrane waveguiding layer 105 where they are most sensitivelydetected. This results in enhanced sensitivity since fewer targetmolecules need to be exposed to the sensor 110 in order to produce apositive response.

There is generally no need for the light source to provide polarizedlight. If unpolarized light is used, two waveguide modes, one fortransverse electric (TE)-polarization where the electric field vector isperpendicular to the plane of incidence, and one for transverse magnetic(TM)-polarization where the magnetic field vector is perpendicular tothe plane of incidence, will be observed at resonance. However,generally, no additional information is gained by the presence of thetwo modes so, for simplicity, as described herein, only one of the twomodes, arbitrarily chosen as the TE mode, is usually excited. Sensor 110also includes a cladding layer 120 between the porous membrane 105 andthe prism 115 for improving confinement of the waveguide mode(s) in theporous membrane 105. Air (or other ambient) or a liquid buffer materialon the other side of porous membrane 105 also provides cladding forporous membrane 105.

In one embodiment of the invention the cladding layer 120 comprises apolymer film, such as a Formvar polymer film. Such a polymer serves toprovide robust attachment of the porous membrane 105 to the prism 115.However, the confinement of the waveguide mode(s) in the porous membrane105 would generally be better if a lower index material were used forcladding layer instead of a polymer cladding layer, such as air in thecase of an air gap.

Light propagating in prism 115 is shown reflecting at the interfacebetween the prism 115 and the cladding layer 120. Reflected light shownas “light out” emerges from the prism 115 and is detected by a suitablephotodetector 130, such as a CCD-based photodetector.

As noted above, system 100 can detect the presence of biological andchemical targets with high sensitivity based on the induced refractiveindex change of the porous membrane 105 when the target molecule isbound to the receptors 108 which can be detected as described above invarious ways, such as a change in the waveguide resonance angle,waveguide resonance wavelength, or intensity of light propagating in theporous membrane. In contrast, conventional technologies for chemical andbiological sensing typically rely on relatively weak interaction ofevanescent fields with molecules on flat surfaces. The limited surfacearea of these conventional sensors, combined with their reliance onevanescent fields, is especially troublesome for the detection of smallmolecules. Conventional sensors (e.g. SPR) are also limited in theirability to detect larger particles (e.g. viruses) due to a loss inevanescence at a distance (e.g. the distal end of a virus) from thesensor surface. Sensors according to embodiments of the presentinvention overcome this disadvantage provided the voids are large enoughto accommodate these larger particles.

Sensors according to embodiments of the invention such as sensor 110have a very large surface area provided by the porous membrane 105.Moreover, such sensors provide excellent field confinement in the porousmembrane 105 where receptors 108 are immobilized, and as described belowrelative to FIG. 2 can be configured to be highly compatible withcurrent commercial sensor instrumentation.

One embodiment for sensors according to embodiments of the inventioninvolves the fabrication of sensor chips that can be directly insertedinto commercial surface plasmon resonance (SPR) sensor instruments. SPRsensor instruments currently dominate the market for biosensingapplications. FIG. 2 shows a depiction of an exemplary porous membranewaveguide sensor system 200 including a porous waveguide sensor 210according to an embodiment of the invention in a sensor “chip”configuration. A sensor 210 in the sensor chip configuration shown inFIG. 2 is adapted for being an independent, potentially disposable,component that can be purchased separately from, and at a lower costthan, the more complex and expensive commercially available or otherwiseknown measurement instrument. Moreover, sensor chip 210 will generallybe cheaper to fabricate and enable lower detection limits for smallmolecules that presently cannot be detected with high accuracy in mostcommercial sensor devices, such as those based on SPR.

Sensor chip 210 includes porous membrane 105, a support layer 118 andcladding layer 120. The sensor chip 210 is generally self supported andcan be an independent, potentially disposable component. The supportlayer 118 makes the sensor chip 210 robust enough to be transported andmanipulated by users, such as for direct insertion into existingmeasurement instrumentation (e.g. SPR-based instrumentation). Theexisting instrumentation (e.g. SPR) generally provides the prism 115 andindex matching layer 119, which is generally a liquid.

In order to couple light into the porous membrane waveguide 105 insystem 200, the refractive index of the prism 115, index matchingmaterial 119, and the support layer 118 should all be about the same.The index matching layer 119 and support layer 118 are effectively anextension of the prism interface so that total internal reflectionoccurs at the support layer/cladding interface. Total internalreflection is generally needed to generate the evanescent field thatallows light to be coupled into the porous membrane waveguide 105.Without the index matching between the prism 115, index matchingmaterial 119, and support layer 118, the evanescent wave might begenerated at the prism interface and die out before reaching thecladding layer 120. Support layer 118 can be embodied as a glass slideor optically transparent plastic or resin, or other material togenerally result in support layer 118 not having a lower refractiveindex than the prism 115.

As with sensor 110 described relative to FIG. 1, absorption losses areminimized by sensor 210 because light is coupled to the porous membranewaveguide 105 through a low loss path comprising prism 115, indexmatching layer 119, support layer 118 and cladding 120, in contrast toarrangements that require coupling of light through high loss paths suchas through thick support layers such as thick (e.g. 500 micron) siliconsubstrates.

As described above, sensors according to embodiments of the inventioncan also utilize grating couplers instead of prisms as the opticalcoupler. This is illustrated in FIGS. 3 and 4. FIG. 3 is a depiction ofan exemplary sensor system 300 including a porous membrane waveguidesensor 110 and a grating coupler 315 according to am embodiment of theinvention for sensing at least one biological target or chemical target.FIG. 4 shows a depiction of an exemplary porous membrane waveguidesensor system 400 including a porous waveguide sensor 210 and a gratingcoupler 315 according to an embodiment of the invention in a sensor“chip” configuration.

The exemplary systems shown in FIGS. 3 and 4 are substantially similarto those described above with respect to FIGS. 1 and 2, respectively.Accordingly, the description above for FIGS. 1 and 2 is sufficient fordescribing the exemplary systems shown in FIGS. 3 and 4, respectively.As described above, in FIGS. 3 and 4, the prism has been replaced withgrating coupler 315. In the embodiments shown in FIGS. 3 and 4, thegrating coupler 315 need not be optically transparent as in the case ofthe optical coupler being a prism described above relative to FIGS. 1and 2. In the various embodiments of the invention, the configuration ofthe grating coupler (i.e., its dimensions, including grating spacing)can be selected to provide a coupling angle that generates one or morewaveguide modes in either of sensors 110 and 210.

The use of grating couplers in the various embodiments of the inventionis not limited to the configurations shown in FIGS. 3 and 4. In someembodiments of the invention, the grating coupler and the membrane canbe fabricated together. That is, the sensor can be fabricated from asingle portion of membrane material in which the plurality of voids areformed on one side and gratings on a second side.

Optical couplers besides prisms or gratings may also generally be usedwith embodiments of the invention. For example, a tapered fiber can beused in place of a prism or grating. Also, as shown by the dashed pathin FIG. 1, light can instead be launched in the waveguide from one endface, instead of the top surface, via butt-coupling with a fiber,end-fire couplings 120, 125 from free-space light focused by a lens, orcoupling from a tapered waveguide. All of these alternatives to prism orgrating-based couplers generally require a measurement of the intensityof light at the opposite end of the waveguide in order to determinewhether target molecules are bound inside the waveguide.

Sensors according to embodiments of the invention can be embodied in awide variety of different embodiments. For example, it is possible todesign such sensors without any solid cladding layers. For example, aflow-through sensor chip can be configured with a fixed thickness airgap between the prism or other optical coupler and the porous membrane.Moreover, although sensors are generally described herein for detectinga specific biological or chemical target, sensors according toembodiments of the invention can include porous membranes comprising aplurality of regions each having different receptors within the voidsprovided in the regions, wherein the different receptors are eachadapted to bind with different targets. For example, a porous membranecan include a plurality of regions which each sense a different target,including control regions. For example, a region of the sensor can beprovided without receptors to provide a control sample in the sensor. Inone embodiment, the respective regions comprise different antibodies,enzymes, cell receptors, molecular print assays, nucleic acids (e.g. DNAor RNA). In another embodiment of the invention, different regions ofthe porous membrane include different functionalities, such asantibodies, enzymes and nucleic acids. Additionally, measurements can beperformed to obtain phase changes.

Moreover, particularly when a silicon-based technology is used, it ispossible for sensors according to embodiments of the invention to behighly integrated. For example, when the substrate comprises silicon,the light source can be disposed on the sensor chip, as well aselectronics including the photodetector. In this embodiment, thephotodetector array can include a plurality of pixels, with one pixelassociated with a particular region of the porous membrane having aparticular receptor. The integrated embodiment can also provide on-chipsignal amplification and signal processing electronics, as well as MEMSdevices, including MEMS mirrors.

Porous silicon membrane waveguide sensors according to embodiments ofthe invention are generally low-cost, high sensitivity sensors that aregenerally capable of detection of wide variety of biological andchemical materials, including simultaneously detecting a plurality ofbiological or chemical materials. Such sensors are generally cheaper andas described above are generally more sensitive than commercial fiberoptic and SPR sensors particularly for low molecular weight species.Applications for sensors according to embodiments of the inventioninclude areas of medicine, environmental monitoring, food safety, andhomeland security. Proof-of-principle operation of the sensor has beendemonstrated using various chemicals and DNA molecules, as described inthe Examples provided below.

EXAMPLES

The following non-limiting Examples serve to illustrate selectedembodiments of the invention. It will be appreciated that variations inproportions and alternatives in elements of the components shown will beapparent to those skilled in the art and are within the scope ofembodiments of the present invention.

The fabrication of a sensor in accordance with an embodiment of theinvention starts with electrochemical etching of an n-type silicon wafer(<100>, 0.01 Ω·cm) in 5.5% aqueous hydrofluoric acid. A current densityof 40 mA/cm² was applied for 35 seconds. The resulting porous siliconmembrane was then removed from the silicon substrate by applying aseries of 5 high current pulses (200 mA/cm² for 4 seconds with 50% dutycycle). This procedure caused electropolishing and subsequent detachmentof the porous film from the substrate. During the electropolishing, aslight widening of the pore diameter at the bottom of the porous siliconmembrane film occurs. FIG. 5 shows a scanning electron microscopy (SEM)image of the resulting porous silicon membrane, evidencing voidscomprising 100 nm diameter pores. In general, 8-10 porous siliconmembranes can be fabricated from the same silicon substrate withoutsignificantly degrading the quality of the resulting porous siliconmembranes.

The porous silicon membrane was then placed on a BK7 glass slide and wasoxidized at 500° C. for 5 minutes in an Omegalux LMF-3550 oven, afterinsertion at 300° C. To build the waveguide structure, 0.25% formvarpolymer in ethylene dichloride was dropped onto the surface of a rutileprism (n=2.1252). Ethylene dichloride is then evaporated to leave behinda thin film of formvar polymer (n−1.5, transparent in infrared region).In order to ensure strong adhesion of the porous silicon membrane to thepolymer film, the membrane was placed at the thinner edge of theethylene dichloride solution drop before the solution completely dried.Using this method, no air gap was formed between the polymer film andthe porous silicon membrane, or between the polymer film and the prism.The porous silicon membrane was placed such that the larger poreopenings were at the air interface to facilitate molecule infiltration.The resulting porous silicon membrane waveguide structure is similar tothat described above with respect to FIGS. 1 and 2.

The resulting porous silicon membrane waveguide was characterized by SEMand by optical measurements. Cross-sectional SEM analysis revealed amembrane thickness of 1 micron with a pore density of approximately5×10⁹ cm⁻². FIG. 6 shows the measurement of the waveguide mode forsimulated and experimental values. Using a Metricon 2010 Prism Coupler,transverse-electric (TE) polarized light from a 1550 nm diode laser wasincident on a cubic zirconium prism at variable angle. The reflectedlight was detected using a germanium photodetector. A waveguide mode isobserved at the angle for which the component of the incident lightwavevector in the prism parallel to the interface matches that of awaveguide mode. At this angle, light is coupled into the waveguide andnot directly reflected back to the photodetector, giving rise to theresonance dip in the measured spectrum shown in FIG. 6. Given themembrane thickness and the polymer refractive index, the membranerefractive index was calculated to be 1.99 and the polymer thickness wasdetermined to be 892 nm by fitting the waveguide mode and substrate modeangles. FIG. 6 shows good agreement between calculated and experimentalvalues. The larger width of the experimental resonance and smallerreflectance amplitude are attributed to scattering losses, which werenot taken into account in the calculation. The waveguide mode measuredis the 1st order TE mode. Reduction the thickness of the porous membraneor using a higher index prism could be used to measure the 0th ordermode.

The sensing operation of the fabricated membrane waveguide isdemonstrated by detection of DNA hybridization. In order to enablespecific detection of complementary DNA oligonucleotides, the fabricatedwaveguide was functionalized by first performing a silanization using 4%aminopropyltriethoxysilane. This was followed by the attachment of amonolayer of the crosslinking chemical, Sulfo-SMCC (Pierce), using waterand ethanol as the solvent. Before attachment in the porous membrane,24-base pair thiol modified probe DNA was reduced for 30 minutes bymixing 1:1 by volume DNA in HEPES buffer with TCEP (Pierce) in water andethanol. In order to screen the negative charges of DNA, which has beenreported to cause oxidation and corrosion of convention porous siliconmembrane sensors upon hybridization, and to enhance DNA infiltration andsurface immobilization, 3 M NaCl was added to the probe DNA solution.Finally, the functionalized porous membrane waveguide sensor was testedthrough exposure to 24-base pair complementary and non-complementary DNA(all solutions included water, ethanol, and 3M NaCl).

FIG. 7 shows the experimental resonance shifts after the fabricatedsensor was exposed to different concentrations of complementary DNA.When the complementary DNA is exposed to the probe DNA immobilized inthe voids, the two DNA strands bind. This hybridization increases theeffective refractive index of the porous silicon membrane, which changesthe waveguide mode dispersion and hence the waveguide resonance anglemeasured using the prism coupler. Larger resonance shifts indicate thata greater number of DNA oligonucleotides are hybridized in the poroussilicon membrane waveguide. FIG. 7 shows resonance shifts to higherangle for all experiments, suggesting the DNA hybridization-enhancedcorrosion problem for conventional p-type porous silicon DNA biosensorsis not present sensors fabricated in accordance with the variousembodiments of the invention. A linear fit of the experimental datashown in FIG. 7 gives the sensitivity of the sensor, which is found tobe 0.048°/uM. Given that the angular resolution of the Metricon prismcoupler is 0.002°, the ultimate detection limit of the porous siliconmembrane waveguide biosensor is 0.002°/(0.048°/uM)=42 nM. Accordingly, aporous membrane waveguide sensor in accordance with the variousembodiments of the invention is capable of nM detection of smallmolecules, not just the nM detection of proteins observed forconventional SPR sensors.

Additionally, control experiments were performed on the fabricatedporous silicon membrane waveguides to demonstrate selectivity. Noresonance shift was observed upon exposure to 1 uM non-complementaryDNA, suggesting that no binding occurred. Furthermore, no resonanceshifts were observed upon exposure to solutions containing only HEPESbuffer, TCEP and 3 M NaCl.

FIG. 8 shows an x-y plot 800 of reflectance as a function of resonanceangle for a sensor in accordance with an embodiment of the invention.The sensor included a 58% porosity, 1.55 micron thick porous siliconmembrane waveguide with polymer cladding before (curve 802) and after(curve 804) attachment of 3-APTES molecules. The reflectance valleys inFIG. 8 corresponds to the angles for which a particular guided mode issupported and will propagate in the waveguide. As shown in FIG. 8, 3distinct modes are supported (1^(st), 2^(nd), and 3^(rd)). As shown inFIG. 8, the attachment of 3-APTES molecules results in a shift inresonance angles for each mode. The first order mode at the largestresonance angle shows the greatest response (0.93 degree shift) tomolecule attachment as compared to the response of the 2^(nd) and 3^(rd)modes (0.83 and 0.56 degree, respectively), suggesting that this mode isthe most sensitive of the three modes.

Optimization of Membrane and Polymer Layer Thicknesses

In order to determine how the detection sensitivity of porous waveguidesin accordance with the various embodiments of the invention variesdepending on the waveguide design parameters, transfer matrix theory andfirst order perturbation theory can be employed. Detection sensitivitycan be defined as the angular shift of the waveguide resonance dividedby the refractive index change of the porous membrane layer due toattachment of small molecules to the void walls. Molecules infiltratedinto the voids induce an overall change in the refractive index of theporous dielectric medium. These dielectric function changes, (z), alsochange the effective index of some waveguide modes, N, in the waveguide.According to perturbation theory, the change of the effective index of awave due to small molecule attachment can be calculated TE waves by:

$\begin{matrix}{{\Delta\left( N^{2} \right)} = \frac{\int_{- \infty}^{\infty}{{{{\Delta ɛ}(z)}\left\lbrack {E(z)} \right\rbrack}^{2}\ {\mathbb{d}z}}}{\int_{- \infty}^{\infty}{\left\lbrack {E(z)} \right\rbrack^{2}\ {\mathbb{d}z}}}} & (1)\end{matrix}$In general, perturbation theory does not generally apply to theinfiltration of liquids that fill the entire volume of the porouswaveguide. The electric field in each layer of the waveguide structureis found based on transfer matrix theory, and the thickness of thecladding layer is optimized to yield deep and narrow waveguideresonances based on a pole expansion method. With Δ∈(z)=2n Δn, Δ(N²)=2NΔN, and N=n_(p) sin θ, an analytical expression of the sensitivity ofthe waveguide for TE modes can be provided as:

$\begin{matrix}\begin{matrix}{{sensitivity} = \frac{\mathbb{d}\theta}{\mathbb{d}n}} \\{= {\frac{\mathbb{d}\theta}{\mathbb{d}N} \cdot \frac{\mathbb{d}N}{\mathbb{d}n}}} \\{= {\frac{\int_{PSi}{\left\lbrack {E(z)} \right\rbrack^{2}\ {\mathbb{d}z}}}{\int_{- \infty}^{\infty}{\left\lbrack {E(z)} \right\rbrack^{2}\ {\mathbb{d}z}}} \cdot \frac{n_{PSi}}{N} \cdot \frac{1}{n_{p}\cos\;\theta}}}\end{matrix} & (2)\end{matrix}$where n_(p) and n_(PSi), are the refractive index of the prism and theporous membrane, respectively, and θ is the resonant angle in the prism.The first term on the right hand side of Eq. (2) is the powerconfinement factor, which is defined as the ratio of the power confinedin the porous membrane layer to the total power distributed throughoutthe entire multilayer waveguide structure. The sensitivity is directlyproportional to the power confinement factor and the incident angle inthe prism.

Based on the mathematical methods described above, the theoreticallycalculated sensitivity as a function of the porosity of a 1.55 m thickpolymer-cladded porous silicon membrane waveguide layer was calculatedand is plotted in FIG. 9A. The corresponding resonance angles are shownin FIG. 9B. In FIGS. 9A and 9B, each curve corresponds to one waveguidemode. Higher order modes can be supported at lower porosities. For eachmode, the sensitivity decreases with increasing porosity of the porousmembrane layer until the mode cutoff condition at the critical angle issatisfied. As the incident angle approaches 90 degrees, the sensitivitygoes to infinity. At very large incident angles, the 1/cos termdominates the power confinement factor in the sensitivity calculation,while the opposite is true at smaller incident angles. If the thicknessof the porous membrane waveguide layer is increased, the curves will beshifted upward and the number of modes supported by the waveguide willalso be increased.

Applicants present certain theoretical aspects above that are believedto be accurate that appear to explain observations made regardingembodiments of the invention based primarily on solid-state devicetheory. However, embodiments of the invention may be practiced withoutthe theoretical aspects presented. Moreover, the theoretical aspects arepresented with the understanding that Applicants do not seek to be boundby the theory presented.

While various embodiments of the present invention have been describedabove, it should be understood that they have been presented by way ofexample only, and not limitation. Numerous changes to the disclosedembodiments can be made in accordance with the disclosure herein withoutdeparting from the spirit or scope of the invention. For example, asshown in FIG. 10, a sensor 1000 can be provided in which sensors areformed only in suspended portions of a membrane material. This structurecan be formed via the use of silicon-on-insulator (SOI) substrates. Insuch structures, before or after forming voids in the upper siliconlayer to define a sensor region, the portion of the silicon oxidecomprising layer beneath the sensor region is removed. Accordingly, airor a liquid buffer is then used as a cladding material on both sides ofthe membrane. Light can then be coupled into the membrane material aspreviously described with respect to FIG. 1. Other configurations arealso possible. Thus, the breadth and scope of the present inventionshould not be limited by any of the above described embodiments. Rather,the scope of the invention should be defined in accordance with thefollowing claims and their equivalents.

Although the invention has been illustrated and described with respectto one or more implementations, equivalent alterations and modificationswill occur to others skilled in the art upon the reading andunderstanding of this specification and the annexed drawings. Inaddition, while a particular feature of the invention may have beendisclosed with respect to only one of several implementations, suchfeature may be combined with one or more other features of the otherimplementations as may be desired and advantageous for any given orparticular application.

The terminology used herein is for the purpose of describing particularembodiments only and is not intended to be limiting of the invention. Asused herein, the singular forms “a”, “an” and “the” are intended toinclude the plural forms as well, unless the context clearly indicatesotherwise. Furthermore, to the extent that the terms “including”,“includes”, “having”, “has”, “with”, or variants thereof are used ineither the detailed description and/or the claims, such terms areintended to be inclusive in a manner similar to the term “comprising.”

Unless otherwise defined, all terms (including technical and scientificterms) used herein have the same meaning as commonly understood by oneof ordinary skill in the art to which this invention belongs. It will befurther understood that terms, such as those defined in commonly useddictionaries, should be interpreted as having a meaning that isconsistent with their meaning in the context of the relevant art andwill not be interpreted in an idealized or overly formal sense unlessexpressly so defined herein.

The Abstract of the Disclosure is provided to comply with 37 C.F.R.§1.72(b), requiring an abstract that will allow the reader to quicklyascertain the nature of the technical disclosure. It is submitted withthe understanding that it will not be used to interpret or limit thescope or meaning of the following claims.

We claim:
 1. A sensor for sensing at least one biological target orchemical target, comprising: a membrane consisting of essentially asingle layer of porous material that supports generation and propagationof at least one waveguide mode, said single layer of porous materialcomprising a plurality of voids having an average size<2 microns; atleast one receptor having structure for binding to said at least one ofsaid biological target or said chemical target within said plurality ofvoids; an optical coupler for coupling light to said membrane sufficientto generate said waveguide mode in said membrane from photons incidenton said optical coupler, the optical coupler selected from the groupconsisting of a prism and a grating; and a cladding separating themembrane and the optical coupler, wherein the cladding is selected fromthe group consisting of an ambient gas layer, a liquid buffer layer, anda layer of polyvinyl formal.
 2. The sensor of claim 1, wherein saidplurality of voids have an average size<0.5 microns.
 3. The sensor ofclaim 1, wherein said single layer of porous material comprises silicon.4. The sensor of claim 1, wherein said single layer of porous materialcomprises at least one of a polymer and a semiconductor.
 5. The sensorof claim 1, wherein the cladding is a single layer.
 6. The sensor ofclaim 1, wherein the at least one receptor comprises at least oneselected from the group consisting of a chemical receptor, abioreceptor, an aptamer, a darpin, a polymer, a biopolymer, a molecularimprint polymer, a biomimetic, an antibody or fragment thereof, anenzyme, a cell receptor, a molecular print assay, and a nucleic acid,and combinations thereof.
 7. The sensor of claim 1, wherein saidmembrane supports generation and propagation of one mode in a wavelengthrange from 1 to 3 microns.
 8. The sensor of claim 1, wherein saidwaveguide mode is at least one of a guided mode and a leaky mode.
 9. Asensing system, comprising: a sensor for sensing at least one biologicaltarget or chemical target comprising a substrate support layer and amembrane supported by the substrate support layer, the substrate supportlayer having at least one opening to expose the membrane and having alower index of refraction than the membrane, the membrane consistingessentially of a single layer of porous material that supportsgeneration and propagation of at least one waveguide mode on saidsupport layer, said single layer of porous material comprising aplurality of voids having an average size<2 microns, and at least onereceptor having structure for binding to said at least one biologicaltarget or chemical target within said plurality of voids; an opticalblock coupler operable for coupling light to said membrane sufficientlyto generate said waveguide mode in said membrane from photonspropagating in said optical block coupler, the optical block couplerselected from the group consisting of a prism and a grating; a claddinglayer separating the membrane and the optical block, wherein thecladding is selected from the group consisting of an ambient gas layer,a liquid buffer layer, and a layer of polyvinyl formal; a light sourcefor providing said photons; and a light detector for detecting saidphotons that are reflected by said optical block coupler.
 10. The systemof claim 9, wherein said substrate support layer and said single layerof porous material both comprise silicon.
 11. The system of claim 9,wherein the optical path for said photons in said optical block couplerto couple to said membrane is exclusive of said substrate support layer.12. The system of claim 9, wherein an optical path for said photons insaid optical block to couple to said membrane is inclusive of saidsubstrate support layer.
 13. The sensor of claim 9, wherein saidwaveguide mode is at least one of a guided mode and a leaky mode.